[Crunch2] [Workbench] Browse and show tools using the GA4GH tool registry API
This first version will just allow users to browse/select public workflows that have been registered at dockstore.org.
The API endpoint should be configurable, though, so that when Arvados supports the tool registry API itself (#9042) users will be able to select tools that are registered in Arvados.
#8 Updated by Radhika Chippada about 5 years ago
tom (on irc):
curl https://www.dockstore.org:8443/api/v1/tools | jq .
#9 Updated by Radhika Chippada about 5 years ago
- Add a “Run a tool” button in the panel header next to “Run a pipeline” in dashboard.
- Add a config parameter to workbench to configure the tool registry end-point
- When this button is pressed, present a “Choose a tool to run” modal similar to “Choose a pipeline to run” to the user
- Get the tool json from the configured end point (do we want to cache this and pull at regular intervals or for each click?)
- Present each version of each tool from the json as a separate link in the popup
pcawg-merge-annotate - master pcawg-merge-annotate - 1.0.0 …
- When a link from the popup is clicked on, show the tool detail in preview pane on the right
- When OK button is selected, create a CR with the selection as mount(s) and take the user to the CR page
- The CR created for the selected tool version will have:
- Name = tool - version (ex: pcawg-merge-annotate - master)
- use mount kind json to store the selection
- store the entire selected tool record including all version as mount point “/var/lib/cwl/tool”
- store the selected tool version as mount “/var/lib/cwl/tool_version”
Out of scope for this story:
- Support for json mount kind
- Presenting appropriate input selection options based on the selected tool description
- Running the selected tool